Introduction

Using data uptill 25th January

pate-rnd xmap-collector --include_file_str 20220119_WC_P1vP6 \
  --include_file_str  20220120_ShakeSpd_1000rpm_Panel1_Plate1 \
  --include_file_str  20220120_ShakeSpd_1200rpm_Panel1_Plate2 \
  --include_file_str  20220120_ShakeSpd_1500rpm_Panel1_Plate3 \
  --include_file_str  20220120_ShakeSpd_1000rpm_Panel2_Plate1 \
  --include_file_str  20220120_ShakeSpd_1200rpm_Panel2_Plate2 \
  --include_file_str  20220120_ShakeSpd_1500rpm_Panel2_Plate3 \
  --include_file_str  20220120_ShakeSpd_1200rpm_Panel2_Plate2 \
  --include_file_str  20220120_ShakeSpd_1500rpm_Panel2_Plate2 \
  --include_file_str  Beta \
  --include_file_str  Interf \
  --include_file_str  PltStd \
  --include_file_str  Endogenous \
  --include_file_str  Exogenous \
  --include_file_str  Platinum \
  --include_file_str  Reproducibility \
  --include_file_str  Donor_Screening \
  --include_file_str  PlatinumStd \
  --include_file_str  HamiltonEquiv\
  --include_file_str  ShakingCompare \
  --include_file_str  20211221_DLS_Matrix_Int \
  --include_sample_str Standard --include_sample_str Buffer --include_sample_str Background --include_sample_str QC --include_sample_str RC  --ignore_case_sample \
  --out_file_name betalot_experiments-2022-01-25.csv
gsutil cp gs://inhouse-xmap-data/user_data_frames/betalot_experiments-2022-01-25.csv ~/'google drive'/'my drive'/projects/beta-av-testing/data/raw/beta-lot-stds-controls-2022-01-25.csv

This notebook aims to explore the distribution of Flexmaps and Hamiltons using the beta lot data. We will -

  1. Extract xMAP controls and standards data
  2. Extract the xmap log
  3. Match the batches we have available hamilton and flexmap information.

Note It looks like the log was only started to collect after 2021-12-02

raw .rmd file stored here

/home/ddhillon/dyson-sync/projects/beta-av-testing/notebooks/process-pseudo-guardbanding/notebooks/02.rmd

Data Import

xMAP Data

Using data uptill 25th January

Batches in xMAP

Log of instruments

Batches in log

Match the log of batches with the batches from xMAP data

Which ones match?

Which ones don’t match?

Some don’t match since the names aren’t exactly the same - we will change these manually. There are still some we’re not able to retrieve xmap data on.

xmap_batches %>% 
  mutate(batch = case_when(batch == "20211214_ShakeComp_Auto_Beta_Panel2_B3" ~ "20211214_ShakingCompare_Auto_Beta_Panel2", 
                           batch == "20211214_Shake_Workcell_Beta_Panel2_B1.csv" ~ "20211214_ShakingCompare_Workcell_Beta_Panel2", 
                           batch == "20211214_Shake_Workcell_Beta_Panel2_B2" ~ "20211214_ShakingCompare_Workcell_Beta_Panel2", 
                           batch == "20211214_Shake_Workcell_Beta_Panel2_B3" ~ "20211214_ShakingCompare_Workcell_Beta_Panel2", 
                           batch == "20211214_Shaking_Auto_Beta_Panel1_B1"  ~ "20211214_ShakingCompare_Auto_Beta_Panel1", 
                           batch == "20211214_Shaking_Auto_Beta_Panel1_B2" ~ "20211214_ShakingCompare_Auto_Beta_Panel1",
                           batch == "20211214_Shaking_Auto_Beta_Panel1_B3" ~ "20211214_ShakingCompare_Auto_Beta_Panel1", 
                           batch == "20211214_Shaking_Workcell_Beta_Panel1_B1" ~ "20211214_ShakingCompare_Workcell_Beta_Panel1", 
                           batch == "20211214_Shaking_Workcell_Beta_Panel1_B2" ~ "20211214_ShakingCompare_Workcell_Beta_Panel1", 
                           batch == "20211214_Shaking_Workcell_Beta_Panel1_B3" ~ "20211214_ShakingCompare_Workcell_Beta_Panel1", 
                           batch == "20210111_PltStd2_Panel1_P3_B1" ~ "20220111_PltStd2_Panel1_P3", 
                           batch == "20210111_PltStd2_Panel1_P3_B2" ~ "20220111_PltStd2_Panel1_P3", 
                           batch == "20210111_PltStd2_Panel1_P3_B3" ~ "20220111_PltStd2_Panel1_P3", 
                           batch == "20220111_PltStd2_Panel2_P3_B1" ~ "20220111_PltStd2_Panel2_P3", 
                           batch == "20220111_PltStd2_Panel2_P3_B2" ~ "20220111_PltStd2_Panel2_P3", 
                           batch == "20220111_PltStd2_Panel2_P3_B3" ~ "20220111_PltStd2_Panel2_P3", 
                           batch == "20220119_WC_P1vP6_P2_Plate2" ~ "20220119_WC_P1vP6_P2_plate2", 
                           TRUE ~ as.character(batch))) %>% 
  inner_join(log_batches)

NOTE
Batches not in pate
1. 20211221_DLS_Matrix_Int_
2. 20220113_1500Shake_TS_
3. 20220124_BufferAdditives_
4. 20220201_AdditivesStds_

Update the above plots after adding this in

Strings that are still not matching

Operator information?

Can we also add in operator information to these experiments?

## # A tibble: 66 × 7
##    date       operator batch description panel_name panel_lot_number
##    <date>     <chr>    <chr> <chr>       <list>     <list>          
##  1 2021-12-02 Connor   2021… 20211202_M… <chr [1]>  <dbl [1]>       
##  2 2021-12-02 Tyler M  2021… 20211202_M… <chr [1]>  <dbl [1]>       
##  3 2021-12-06 Connor   2021… 20211206_E… <chr [1]>  <dbl [1]>       
##  4 2021-12-06 Connor   2021… 20211206_E… <chr [1]>  <dbl [1]>       
##  5 2021-12-06 Tyler M  2021… 20211206_E… <chr [1]>  <dbl [1]>       
##  6 2021-12-06 Tyler M  2021… 20211206_E… <chr [1]>  <dbl [1]>       
##  7 2021-12-14 Connor   2021… 20211214_S… <chr [1]>  <dbl [1]>       
##  8 2021-12-14 Connor   2021… 20211214_S… <chr [1]>  <dbl [1]>       
##  9 2021-12-14 Tyler M  2021… 20211214_S… <chr [1]>  <dbl [1]>       
## 10 2021-12-14 Tyler M  2021… 20211214_S… <chr [1]>  <dbl [1]>       
## # … with 56 more rows, and 1 more variable: instrument_name <chr>

Viz

QCs

Which experiments had QCs on them?
10 experiments?

5 experiments had RCs on them (log was started on 20211202 so any experiments with RCs on them prior to that aren’t in this list currently)

We have more data on the latest controls so we will look at those

Plots out all the RCs for each flexmap and hamilton

Flexmap x-axis

FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2

[[1]] NULL

[[2]] NULL

[[3]] NULL

[[4]] NULL

[[5]] NULL

[[6]] NULL

[[7]] NULL

Hamilton x-axis

FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2

[[1]] NULL

[[2]] NULL

[[3]] NULL

[[4]] NULL

[[5]] NULL

[[6]] NULL

[[7]] NULL

Recoveries

Experiments with recoveries

Flexmap x-axis

FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2

[[1]] NULL

[[2]] NULL

[[3]] NULL

[[4]] NULL

[[5]] NULL

[[6]] NULL

[[7]] NULL

Hamilton x-axis

FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2

[[1]] NULL

[[2]] NULL

[[3]] NULL

[[4]] NULL

[[5]] NULL

[[6]] NULL

[[7]] NULL

Operator specific comparison

FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2

[[1]] NULL

[[2]] NULL

[[3]] NULL

[[4]] NULL

[[5]] NULL

[[6]] NULL

[[7]] NULL

Bead counts

Flexmap x-axis

Hamilton x-axis

FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2

[[1]] NULL

[[2]] NULL

[[3]] NULL

[[4]] NULL

[[5]] NULL

[[6]] NULL

[[7]] NULL